as far as i can see, actually no one has answered your question.
A reference to a footnote can look like this:
<p class="does not matter"><a href="#footnote1" id="position1">Some visible text</a></p>
The footnote with a backward reference like this
<p class="footnoteclass"><a href="#position1" id="footnote1">Some visible text</a>more footnote text</p>
This works fine for me (well, at xhtml/epub, i dont know what kindel does with this)
How to get there with regex: I do not think that it's possible in one step, try to split the job, and exchange only parts of then string in one step. And there isn't a sample of your footnotes, so i can't see if there is alread a reference to jump back.
to your css: What is line-hight: 0.78 ?? millimeters, centimeters, kilometers ? :-)